grinch | global report investigating novel coronavirus haplotypes

B.1.351 report 2021-01-03



Data source and processing

This report is recent as of 2021-01-03 14:18 GMT. All SARS-CoV-2 sequences were downloaded from GISAID and genomes were de-duplicated based on GISAID sequence name – note that the publically available metadata may not fully allow us to de-duplicate by patient. Full data processing pipeline found here.

The sequences were then assigned lineages with pangolin v2.1.6, pangoLEARN version 2020-12-17-2.

Pangolin assigns B.1.351 to any sequences with more than 5 of the 9 defining B.1.351 SNPs, defined in the preprint here.

Table 1 | Summary of data

Lineage Country count Country Sequence count Earliest sequence Travel history
B.1.351 4 South_Africa 349, Switzerland 2, Finland 1, UK 1 353 2020-10-08

Lineage B.1.351

Caveat: Most locations outside the original focus have not reported sustained transmission and many cases have known travel links to the focal location. Increasing numbers of international cases is currently likely due to increased surveillance and vigilance.

Table B.1.351 | Lineage B.1.351

Statistic Information
Count 353
Likely origin South Africa
SNPs aa:E:P71L
aa:N:T205I
aa:orf1a:K1655N
aa:S:D80A
aa:S:D215G
aa:S:K417N
aa:S:A701V
aa:S:N501Y
aa:S:E484K

Figure 1 | Cumulative sequence count over time B.1.351

2021-01-03T17:54:51.544180 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 2 | Date of earliest B.1.351 detected

2021-01-03T17:54:50.998532 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 3 | Map of B.1.351 sequence counts

2021-01-03T17:54:51.226165 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 4 | Sequence count per country B.1.351

2021-01-03T17:54:51.371334 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 5 | Frequency B.1.351 in sequences produced since first new variant reported per country

2021-01-03T17:54:51.669492 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 6 | B.1.351 count per country

2021-01-03T17:54:52.018315 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Figure 7 | Rolling average B.1.351 frequency per country

2021-01-03T17:54:51.804351 image/svg+xml Matplotlib v3.3.3, https://matplotlib.org/

Table 2 | Reported B.1.351 imports.

Country count: 8

Country Earliest report Date local transmission Local transmission Source
South Africa 2020-10-08 2020-10-08 1 https://www.medrxiv.org/content/10.1101/2020.12.21.20248640v1
United Kingdom 2020-12-12 2020-12-20 1 https://travelhealthpro.org.uk/news/561/covid-19-variant-south-africa-two-cases-reported-in-the-united-kingdom
Switzerland 2020-12-14 0 https://www.swissinfo.ch/eng/south-african-covid-variant-reported-in-southern-switzerland/46257338
Finland 2020-12-19 0 https://news.sky.com/story/covid-19-finland-reports-cases-of-new-variants-first-identified-in-uk-and-south-africa-12173983
Zambia 2020-12-30 2020-12-30 1 https://twitter.com/danieljbridges/status/1344227535870164992
France 2020-12-31 0 https://www.france24.com/en/france/20201231-france-detects-first-case-of-south-african-strain-of-covid-19
Japan 2020-12-19 0 https://www.japantimes.co.jp/news/2020/12/29/national/japan-south-africa-variant/
Australia 2020-12-22 0 https://news.sky.com/story/australia-reports-its-first-case-of-south-africa-coronavirus-variant-12174611